tbuckley/cabot-search huggingface dataset:
EPCO-40. CARM1 IS A NOVEL TUMOR SUPPRESSOR IN GLIOBLASTOMA THAT REGULATES QKI THROUGH ARGININE METHYLATION
Authors: Kaylene Lu, Tanner Wright, Seula Shin, Mark Bedford, Jian Hu
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is the most common form of primary brain tumor, characterized by dismal patient prognosis. Current pharmacological interventions have not significantly improved patient outcomes due to intratumor heterogeneity and the persistence of glioma stem cells (GSCs) that drive invasion and resistance. Thus, treatment strategies based on a deeper molecular understanding of gliomagenesis are urgently needed. Quaking (Qki, encoded by the gene Qk) is frequently altered in GBM; Qk mutations or deletions occur in 35% percent of cases, and the Qki protein is absent in 50-60% of cases. Our lab found that deletion of Qk in Trp53-/-; Pten-/- pre-malignant neural stem cells (NSCs) enables them to expand outside their niche and develop into malignant GBM. Mechanistically, we determined that Qki functions as a transcriptional coactivator of lipid metabolism genes in the central nervous system, where loss of Qki dysregulates the lipidome and alters cellular membrane integrity. While several downstream processes governed by Qki have been delineated, upstream regulators of Qki remain unknown. Recurrent cancer mutations to specific Qki arginine residues implicate the dysregulation of arginine methylation, and previous studies indicate that proteins in the same family as Qki can be methylated by protein arginine methyltransferases (PRMTs). Utilizing in vitro methylation assays, we demonstrate that Qki is selectively methylated by the PRMT coactivator-associated methyltransferase 1 (CARM1) in the Quaking regulatory domain (QRD), where cancer mutations were reported. Within the QRD, we identified arginine 242 (R242) and arginine 256 (R256) as specific CARM1-mediated methylation sites on Qki. Mutations to these sites compromise Qki transcriptional activity, as Qki methylation mutant-expressing GSCs exhibited downregulation of Qki target genes compared to those expressing wildtype Qki. Taken together, we provide evidence that CARM1 functions as a tumor suppressor in GBM through a novel mechanism of Qki dysregulation.
DNAR-09. THE ROLE OF <i>MSH2</i> IN GLIOBLASTOMA GROWTH AND TEMOZOLOMIDE RESISTANCE
Authors: Montserrat Puigdelloses-Vallcorba, Alice Buonfiglioli, Gonzalo Pinero, Zhihong Chen, Dolores Hambardzumyan
Journal: Neuro-Oncology (2023)

Abstract Despite all the advances in understanding and finding new therapeutic approaches, glioblastoma (GBM) remains incurable. The standard of care is surgical resection when feasible, combined with radiotherapy and chemotherapy using temozolomide (TMZ). Different mechanisms have been suggested to contribute to this failure: intrinsic or acquired resistance to TMZ and deficiencies in DNA mismatch repair (MMR) genes such as MSH2 that promote tumor progression. In this study, we have identified a correlation between low MSH2 expression and shorter patient survival utilizing patient GBM samples from the TCGA. Furthermore, we have generated immunocompetent genetically engineered mouse models (GEMMs) of GBM with germline or somatic loss of Msh2 to test the biological significance of Msh2 in GBM growth and resistance to TMZ and immunotherapy. We have generated tumors with reduced or abrogated Msh2 using GEMMs based on the RCAS/tv-a gene transfer system in combination with mice that exhibited heterozygous and homozygous loss of Msh2. Tumors with overexpression of PDGFB in combination with Tp53 silencing in mice with reduced or deficient Msh2 demonstrated shorter survival time and increased tumor growth compared to wild-type tumor-bearing mice. In addition, our results indicate that Msh2 deficiency increases the malignancy of gliomas. Finally, our data demonstrate that TMZ treatment for two weeks provides a significant survival advantage in WT tumor-bearing mice, while no efficacy was observed in tumor-bearing mice with either heterozygous or homozygous loss of Msh2, recapitulating what is observed in clinics. We are currently evaluating the role of Msh2 in the efficacy of immune checkpoint inhibitors in GBM.
MODL-28. LIVING EX VIVO ORGANOTYPIC BRAIN SLICE CULTURES AS A COMPREHENSIVE SUBSTRATE FOR TUMOR ENGRAFTMENT AND ANALYSIS
Authors: Adebimpe Adefolaju, Breanna Mann, Xiaopei Zhang, Noah Bell, Morrent Thang, Rajaneekar Dasari, Krishna Kanchi, Alain Valdivia, Yang Yang, Andrew Buckley, Vivien Lettry, Carolyn Quinsey, Yasmeen Rauf, David Kram, Noah Cassidy, Cyrus Vaziri, David L Corcoran, Stephen Rego, Yuchao Jiang, Lee M Graves, Denise Dunn, Scott Floyd, Albert Baldwin, Shawn Hingtgen, Andrew B Satterlee
Journal: Neuro-Oncology (2023)

Abstract Heterogeneity, drug resistance, tumor infiltration, and invasiveness significantly contribute to the poor prognosis often associated with brain cancers. To enhance drug development, it is crucial to have models that accurately replicate human responses. Standard in vitro methods to culture, treat and analyze brain tumors often lack resemblance to the original tumor and provide limited insight. To address these challenges, we developed an organotypic brain slice culture (OBSC) model that recapitulates in vivo tumor characteristics within a functional tumor microenvironment (TME) and provides rapid results. OBSCs effectively measure engrafted tumor growth, morphology, and invasion rates. Furthermore, engrafted tumors can undergo relevant therapeutic treatments and be analyzed for drug outcomes. In a 4-day assay, we successfully engrafted a diverse range of brain cancer cell lines, including low-passage lines that struggle to establish in vivo. These cell lines maintain tumor-specific invasion patterns, interact with the OBSC microenvironment, and display killing patterns consistent with in vivo tumor responses. Notably, invasive, metastatic, and diffuse tumor cell lines migrate outward on OBSCs, while densely growing lines contract inward. To further validate OBSCs as a model for the TME, we treated MB231BR, LN229, and U373 tumor lines with TR107, an experimental ClpP inhibitor derived from ONC201. This therapeutic family maximizes tumor elimination by targeting normal cells within the TME. In vitro experiments showed TR107 achieving incomplete tumor kill on cell lines grown in vitro, whereas treatment on OBSCs led to complete tumor kill, suggesting OBSCs' contribution to TME-based tumor elimination. Conclusively, OBSCs provide a valuable platform for studying brain cancers and accurately replicating tumor behavior and responses to therapies within the TME. This model has the potential to advance drug development and deepen our understanding of brain cancer biology, ultimately improving prognoses and treatment outcomes for patients.
CNSC-11. SEIZURE PRESENTATION IN IDH WT GLIOMA IS RELATED TO UPREGULATED SYNAPTIC SIGNALING AND IONIC TRANSPORT GENES
Authors: Malcolm McDonald, Abdul Khan, Prazwal Athukuri, Brittney Lozzi, Benjamin Deneen, Jacob Mandel, Ganesh Rao
Journal: Neuro-Oncology (2023)

Abstract Isocitrate dehydrogenase wildtype (IDH WT) glioblastoma (GBM) is the most common malignant brain tumor in adults and is universally lethal. Seizures often occur as a presenting sign of tumor. Recent studies have implicated tumor-neuron communication facilitating synaptic remodeling and peritumoral circuit hyperactivity influencing tumor growth. We assessed the clinical and transcriptional effect of seizure presentation on GBM biology. 63 tumor samples were analyzed for clinical characteristics. Bulk RNA sequencing data was used to identify differentially expressed genes (DEGs), gene sets enrichment analysis (GSEA), and gene ontologies (GO). 24 IDH WT GBM patients presented with seizures compared to 39 patients presenting with other symptoms. There were no significant differences between age at presentation, sex, tumor lobe, tumor location, or grade of tumor. GSEA of gene ontologies revealed upregulated genes in the seizure cohort were largely related to synaptic signaling, ionic transport, and receptor signaling (p-val&amp;lt; 0.05). Alternatively downregulated gene sets were related to extracellular matrix organization, and inflammatory and immune response (p-val&amp;lt; 0.05). Focusing on significantly upregulated DEGs (padj&amp;lt; 0.05,) biological processes related to glutamatergic synaptic transmission and cellular components related to synaptic structures were upregulated. Alternatively, significantly downregulated DEGs (padj&amp;lt; 0.05) were related to biological processes of immunity and extracellular matrix organization and cellular components related to the extracellular matrix. Upregulated genes include IGFN1 and THBS4, both involved in synapse assembly, and SLC17A3, involved in presynaptic glutamate sorting (Log2FC &amp;gt;1,padj &amp;lt;0.05). The downregulated genes include numerous collagen related genes and immune related genes and KCNJ15, an inward rectifying potassium channel and GABRR1, a GABA-rho subunit. Using bulk RNA sequencing in a clinically similar set of IDH WT tumors, we found gene sets and gene ontologies related to synaptic signaling and glutamatergic signaling upregulated in patients with seizures while genes related to both extracellular matrix and immune inflammation were downregulated.
BIOM-13. ASSOCIATION OF HAND-FOOT SKIN REACTIONS WITH SURVIVAL IN RECURRENT GLIOBLASTOMA PATIENTS TREATED WITH REGORAFENIB
Authors: Jan-Michael Werner, Peter Hau, Thomas Kowalski, Hannes Treiber, Patrick Roth, Michael Wollring, Isabelle Stetter, Caroline Tscherpel, Elena Rosen, Garry Ceccon, Claudia Chapuy, Uwe Schlegel, Michael Weller, Gereon Fink, Norbert Galldiks
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION The phase 2 REGOMA trial suggested a survival benefit of the multikinase inhibitor regorafenib for treating patients with glioblastoma at first recurrence. Hand-foot skin reactions (HFSR) following multikinase inhibitor therapy have been reported to predict prolonged overall survival (OS) in patients with solid tumors. The predictive value of HFSR in patients with recurrent glioblastoma undergoing regorafenib therapy remains to be investigated. METHODS Fifty-seven patients (age range, 35-77 years) with recurrent IDH-wildtype glioblastomas were retrospectively identified from five centers in Germany and Switzerland. Regorafenib was administered at 160 mg/d for the first three weeks of each 4-week cycle, with individual dose adjustments according to toxicity. Patients were stratified into two groups based on the occurrence of HFSR following regorafenib. Group differences were investigated using the Mann-Whitney rank-sum and Fisher's exact tests. Kaplan-Meier analysis was used for univariate analyses, and the Cox proportional hazards regression model for multivariate analyses. RESULTS Patients received a median of two regorafenib cycles (range, 1-14 cycles). Median follow-up after recurrence was 7.0 months (range, 0.6-35.9 months). The median number of previous treatment lines was 2 (range, 1-6 lines). At the time of data analysis, 47 patients (82%) had died. HFSR were observed in 14 out of 57 patients (25%) and associated with a significantly longer OS (10.6 vs. 6.0 months; P = 0.040). No significant group differences (HFSR compared to no HFSR) were observed regarding age, the extent of resection, MGMT promoter methylation, Karnofsky performance status, or the number of completed regorafenib cycles (all P &amp;gt; 0.05). Cox proportional hazards regression analysis confirmed that HFSR were associated with longer OS (P = 0.039; HR, 0.438), independent of age, Karnofsky performance status, and the number of previous treatment lines (all P &amp;gt; 0.05). CONCLUSION Our data suggest that the occurrence of HFSR following regorafenib is associated with longer OS in recurrent glioblastoma patients.
EPID-32. A COST ANALYSIS OF BRAIN AND NERVOUS SYSTEM CANCER CARE: AN EXAMINATION OF HEALTHCARE EXPENDITURE TRENDS IN THE UNITED STATES FROM 1996 TO 2016
Authors: Edward Guo, Mehul Gupta, Heather Rossong, Shubidito Ahmed, Igor Stukalin, Sanju Lama, Garnette Sutherland
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Management of brain and central nervous system malignancies is associated with substantial healthcare spending, yet estimates of per-patient cost and longitudinal temporal trends remain elusive. In this study, we investigate trends in United States (US) healthcare spending on these diseases between 1996-2016. METHODS We utilize inflation-adjusted national healthcare spending data and age-adjusted prevalence estimates from the Institute for Health Metrics and Evaluation to estimate per-patient US healthcare spending stratified by age and care setting. We employ joinpoint regression to identify temporal trends in healthcare spending, expressed as annual percent change (APC). Drivers of change data from 1996-2013 were evaluated to investigate shifts associated with increased spending. RESULTS In 2016, total healthcare spending attributable to brain and nervous system cancers was $6.85 billion (95% CI, $5.98-7.57 billion), corresponding to $2,245 (95% CI $1,962-$2,480) per patient, with the largest share coming from inpatient care settings ($4.60 billion [95% CI 3.87-5.24 billion]). Private payers shouldered the majority of costs (65.6%) compared to public payers (28.1%) and out-of-pocket expenses (6.4%). The average APC in spending between 1996-2016 was 3.69% [95% CI 3.00%-4.39%], driven primarily by an increase in the price and intensity of inpatient care (11.8% [95% CI 7.7%-16.1%). Further, three statistically significant periods of spending change were identified: 1996-2005 (2.42% [95% CI 2.04-2.80%], p &amp;lt; 0.001 ), 2005-2008 (4.43% [95% CI 1.08%-7.89%], p &amp;lt; 0.0001), 2008-2014 (6.32% [95% CI 5.41%-7.25%], p &amp;lt; 0.001), with spending being relatively stable from 2014-2016. DISCUSSION US expenditures for brain and nervous system malignancies are substantial and have significantly increased between 1996-2016, largely driven by increased inpatient spending. These findings may inform policy efforts to reduce the disease burden while balancing healthcare spending.
BIOM-12. ULTRA-DEEP WHOLE GENOME SEQUENCING UNCOVERS A HIGH PREVALENCE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA
Authors: Hunter Underhill, Andrew Farrell, Charlie Dean, Brion Harrison, Mary Bronner, Howard Colman, Randy Jensen
Journal: Neuro-Oncology (2023)

Abstract The detection of glioblastoma-derived circulating cell-free DNA (ccfDNA) has proven formidable because tumor-specific mutations are hidden among the abundance of ccfDNA from healthy cells. While capture-enrichment panels provide the necessary read depth to detect low-frequency variants, searches are constrained to a narrow range of targets and largely limited to single nucleotide variants (SNVs). Here, we use ultra-deep whole genome sequencing (WGS) to broaden the search for somatic mutations across the entire genome. In addition, a kmer-based reference-free variant caller, which mitigates the bias and errors that accrue during alignment, is used to extend the mutation search beyond SNVs to include insertions/deletions (INDELS) and structural variants (SVs) such as large INDELS ( &amp;gt;20 bp) and tandem duplications. In tumor DNA and ccfDNA, we achieve a WGS (GRCh38) mean read depth of 263X and 225X, respectively. WGS of matched buffy coat DNA and sequencing reads from the 1000 Genome Database were used to eliminate germline polymorphisms, sequencing artifacts, and common variants. We detected 20,488 somatic mutations in tumor DNA of which 17.3% affected a coding sequence, 31.9% were INDELS, 91 were large INDELs, and 18 were tandem duplications. A tumor-informed search identified 489 of these somatic mutations in ccfDNA which included a large INDEL and a similar portion of mutations affecting a coding sequence. Using an unguided search for glioblastoma-derived ccfDNA uncovered an additional 8,794 somatic mutations of which 16.6% involved a coding sequence, 60.7% were INDELS, 30 were large INDELS, and 3 were tandem duplications. The high prevalence of somatic mutations discovered in ccfDNA using an unbiased approach highlights the low yield of tumor-informed searches in spatially genetically heterogeneous cancers like glioblastoma. Our findings demonstrate that ultra-deep WGS detects glioblastoma-derived ccfDNA by broadening the search for variants across the entire genome and through the inclusion of INDELS and SVs.
DDDR-02. THE EFFICACY OF SOTORASIB IN KRAS-MUTATED NSCLC PATIENTS WITH BRAIN METASTASES: A RETROSPECTIVE COHORT STUDY
Authors: Anna Lebouille-Veldman, Trent Taros, Noah Nawabi, Luke Peng, John Philips
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Sotorasib has emerged as a favorable treatment option for patients with advanced KRAS-mutated non-small cell lung cancer (NSCLC) including those with brain metastases (BM). The objective of this study was to determine the efficacy of sotorasib in the treatment of pre-treated BMs in patients with NSCLC. METHODS This retrospective cohort study included adult patients with KRAS-mutated NSCLC with BMs who received sotorasib between April-2021 and March-2023 at Mass General Brigham Hospitals. Intracranial progression-free survival (ICPFS) and overall survival (OS) were the primary endpoints and were explored using Kaplan Meier analyses for three groups of patients: patients with active BMs and no local therapy (1), patients with active BMs with local treatment within one month of sotorasib initiation (2) and patients with radiographically stable BMs following previous local treatment (3). RESULTS 31 patients with NSCLC and BMs were included (23% male). Mean age at start of sotorasib was 60. 87% of patients had primary lung adenocarcinoma, and 68% of patients had between 1 and 4 BMs when they started sotorasib. Differences in survival distributions for ICPFS for patients in each of the three groups were statistically significant, χ2(2) = 7.600, p = 0.022. Median ICPFS was 3 months (95% CI: 0 – 8.9) from start of sotorasib for group 1, 5 months (0-11.5) group 2, and 15 months (0-33.5) for group 3. Median OS was 4 months (0-8.8) for group 1, 6 months (0-13.7) for group 2, and 12 months (3.6-20.4) for group 3. 55% of patients experienced intracranial progression on sotorasib, including 39% of patients who had stable BMs at sotorasib initiation. CONCLUSION The results of this study indicate that while sotorasib does have intracranial activity, a multimodal approach to BM therapy is still warranted, as are future studies with larger patient samples, controls, and extended follow up.
BIOM-23. IDENTIFICATION OF NOVEL BIOMARKERS FOR BRAIN TUMOR USING PRECISION MEDICINE APPROACHES: ORC6 PLAYS A CRITICAL ROLE IN GLIOBLASTOMA THERAPEUTICS
Authors: Pei-Chi Chang, Jin-Hong Huang, Yao-Feng Li
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Brain tumors remain challenging to treat despite diagnostic advancements. Current approaches involving surgery, radiotherapy, and chemotherapy tend to fail due to drug resistance. Our team identified potential biomarkers associated with aggressive brain tumors, including ORC6 and GPC4. ORC6, implicated in DNA replication and overexpressed in many cancers, presents a promising therapeutic target. In this study, we leverage advanced bioinformatics and experimental validation to further elucidate ORC6's potential for cancer treatment. Material and methods: This study uses R programming and packages to identify biomarkers from genomic databases like TCGA, CGGA, and GLASS. Protein expression is also assessed via tissue microarray and immunohistochemistry. Changes in the ORC6 gene are studied using GO, KEGG, and gene set enrichment analysis techniques. The tumor microenvironment is predicted using CIBERSORT. RESULTS are presented with 3D CLARITY images, and a deep learning algorithm is introduced for potential clinical application optimization. RESULTS Utilizing bioinformatics analyses, we identified ORC6 and GPC4 as potential biomarkers impacting tumor growth. This study focuses on ORC6, which demonstrated significantly increased expression in IDH-wildtype astrocytoma versus normal brain tissue. This heightened ORC6 expression correlated with tumor grading, poor prognosis, and increased KI67 expression in all glioma subgroups. ATAC sequencing and gene set enrichment analysis revealed E2F factors as potential ORC6 regulators and showed that increased ORC6 expression affected cell proliferation signaling pathways. Single-cell sequencing data further indicated ORC6 expression correlation with tumor cells, proliferative stem cells, and M0, M1, and M2 macrophages. Additionally, high ORC6 expression was observed in several brain tumor cell lines (U87MG, U118MG, LN229, GBM8401) that could be down-regulated using siRNA, paving the way for more complex gene editing and functional modeling experiments. CONCLUSION This study employs sophisticated bioinformatics and experimental validation techniques to explore the potential of targeting ORC6 for cancer therapy. Keywords: ORC6, Glioblastoma, TCGA, CGGA, GLASS, biomarker
DNAR-10. HETEROGENEOUS MGMT PROMOTER METHYLATION IN A MULTIFOCAL GLIOBLASTOMA: A CASE REPORT
Authors: Emily Sloan, Joseph Watson, Peter Ahn, Ann Jay, Matthew Minor, Edina Komlodi-Pasztor
Journal: Neuro-Oncology (2023)

Abstract MGMT promoter methylation status is an important predictive biomarker for treatment response in glioblastoma. MGMT unmethylated glioblastoma has elevated levels of MGMT which ultimately leads to chemoresistance. Clinicians consider the MGMT methylation status when treatment recommendations are given, and clinical trials use this marker for the selection of a homogenous group of glioblastoma patients based on prognosis. Here, we present a case of multifocal glioblastoma with heterogeneous MGMT methylation status. A 56-year-old male presented with left leg weakness for 2 months and left arm weakness for 1 month. Imaging revealed a calcified, rim enhancing right temporoparietal cystic lesion and a heterogeneously enhancing right parietal mass. Perilesional edema surrounded and connected the two lesions. The patient underwent gross total resection of the parietal mass and pathology revealed a WHO grade 4 glioblastoma, IDH wildtype, unmethylated tumor. Postoperatively, the patient was neurologically intact. He completed a 6-week long course of concomitant chemoradiation without any significant side effects. Two weeks later the patient developed rapidly worsening headaches, nausea, vomiting, dizziness, and left side weakness. Imaging revealed significant enlargement of the previously unresected temporoparietal cystic lesion with marked increase in surrounding edema and a 2-3 mm right to left midline shift. Patient underwent craniotomy with cyst drainage and tumor resection of the right cystic temporoparietal lesion, demonstrating a WHO grade 4 glioblastoma, IDH wildtype, methylated tumor. Post-operatively the patient was again neurologically intact and started adjuvant temozolomide. MGMT methylation status of glioblastoma can alter recommendations for chemotherapy with temozolomide. MGMT methylation status might vary in distinct parts of the tumor as molecular heterogeneity is a hallmark of glioblastoma. This heterogeneity should be considered by clinicians when treatments are recommended and by clinical trials for glioblastoma patients, especially when multifocal lesions have a distinct radiographic appearance.